Analyses with Subsets of Nuclear Genes

Among trees based on subsets of nuclear genes, the tree based on protein-coding genes only was most similar to the tree for the complete nuclear data set. All branching relationships were identical except that Primatomorpha received higher support (posterior probability = 0.58) than Scandentia + Dermoptera (posterior probability = 0.42). Euarchonta was still supported, but the posterior probability was only 0.56.

Analyses with the remaining partitions of the nuclear data (UTRs; 1st and 2nd codon positions; 3rd codon positions + UTRs) resulted in trees with more topo-logical differences. Posterior probabilities remained high for some clades, but were lower in other cases. Posterior probabilities were 1.00 for the four major groups (Xenarthra, Afrotheria, Laurasiatheria, Euarchontoglires) and for Boreoeutheria. At the base of the tree, Xenarthra + Boreoeutheria was strongly supported by 3rd codon positions + UTRs (posterior probability = 0.98); other partitions did not resolve the root of the placental tree with high probabilities (i.e., >0.95). Within Afrotheria, Paenungulata, Tubulidentata + Macroscelidea + Afrosoricida, Macroscelidea + Afrosoricida, and Afrosoricida were generally supported. Within Euarchontoglires, posterior probabilities for Glires ranged from 0.02 to 1.00 with different partitions. Posterior probabilities for Euarchonta were lower than for Glires and ranged from 0.02 (UTRs only) to 0.88 (UTRs + 3rd codon positions). Within Euarchonta, 3rd codon positions + UTRs supported Scandentia + Dermoptera (posterior probability = 0.99) whereas, 1st + 2nd codon positions favored Primatomorpha (posterior probability = 0.77). Within Laurasiatheria (Table 4), Variamana was supported by 1st + 2nd codon positions of nuclear genes (posterior probability = 1.00). Chiroptera+ Eulipotyphla was not supported by any of the partitions of the nuclear genes. Support for Fereuungulata was not evident in analyses with UTRs, 1st + 2nd codon positions, and UTRs + 3rd codon positions. Carnivora + Pholidota was consistently supported in analyses with different nuclear partitions.

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